PDB Short entry for 3KK9 HEADER TRANSFERASE 04-NOV-09 3KK9 TITLE CAMKII SUBSTRATE COMPLEX B COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM/CALMODULIN DEPENDENT PROTEIN KINASE II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAMKII KINASE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: UNC-43, K11E8.1, K11E8.1D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAMKII, ATP-BINDING, KINASE, NUCLEOTIDE-BINDING, SERINE/THREONINE- KEYWDS 2 PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KURIYAN,L.H.CHAO,P.PELLICENA,S.DEINDL,L.A.BARCLAY,H.SCHULMAN REVDAT 4 13-OCT-21 3KK9 1 SEQADV LINK REVDAT 3 26-MAY-10 3KK9 1 AUTHOR REVDAT 2 23-MAR-10 3KK9 1 JRNL REVDAT 1 09-FEB-10 3KK9 0 JRNL AUTH L.H.CHAO,P.PELLICENA,S.DEINDL,L.A.BARCLAY,H.SCHULMAN, JRNL AUTH 2 J.KURIYAN JRNL TITL INTERSUBUNIT CAPTURE OF REGULATORY SEGMENTS IS A COMPONENT JRNL TITL 2 OF COOPERATIVE CAMKII ACTIVATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 264 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20139983 JRNL DOI 10.1038/NSMB.1751 REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 5153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.272 REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.329 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.580 REMARK 3 FREE R VALUE TEST SET COUNT : 236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7870 - 4.0380 1.00 2539 119 0.2490 0.2990 REMARK 3 2 4.0380 - 3.2060 0.95 2378 117 0.3100 0.3860 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 63.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.760 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 65.11400 REMARK 3 B22 (A**2) : -37.62200 REMARK 3 B33 (A**2) : -27.49200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 17.36300 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2257 REMARK 3 ANGLE : 0.798 3062 REMARK 3 CHIRALITY : 0.053 336 REMARK 3 PLANARITY : 0.003 392 REMARK 3 DIHEDRAL : 15.927 817 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -13.7108 -16.3141 -19.2794 REMARK 3 T TENSOR REMARK 3 T11: 0.0350 T22: 0.3536 REMARK 3 T33: 0.2581 T12: -0.0078 REMARK 3 T13: 0.0312 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.1008 L22: 3.1507 REMARK 3 L33: 2.2915 L12: 0.0876 REMARK 3 L13: 0.4936 L23: -0.3188 REMARK 3 S TENSOR REMARK 3 S11: -0.1150 S12: 0.4115 S13: -0.1052 REMARK 3 S21: -0.1861 S22: -0.0365 S23: 0.0250 REMARK 3 S31: -0.2236 S32: 0.1134 S33: -0.0547 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5171 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% 2-METHYL-2,4-PENTANEDIOL, .1M REMARK 280 POTASSIUM CHLORIDE, 5MM MAGNESIUM SUFLATE, 50MM 4-(2- REMARK 280 HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID, PH 7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.23500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -37.70800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 273 REMARK 465 GLU A 274 REMARK 465 ARG A 275 REMARK 465 VAL A 276 REMARK 465 ALA A 277 REMARK 465 SER A 278 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 16 -137.24 -112.45 REMARK 500 PHE A 24 28.55 40.78 REMARK 500 ALA A 61 -70.56 -38.88 REMARK 500 VAL A 73 104.83 -39.85 REMARK 500 GLU A 82 -82.30 56.84 REMARK 500 ASP A 90 139.28 -39.28 REMARK 500 GLU A 105 -56.19 68.54 REMARK 500 SER A 108 -177.08 -68.84 REMARK 500 ARG A 134 -38.56 79.26 REMARK 500 ASN A 135 48.03 -109.48 REMARK 500 ALA A 144 -50.69 -27.87 REMARK 500 ASP A 156 74.17 46.02 REMARK 500 ALA A 160 140.03 -39.97 REMARK 500 ASN A 164 -144.01 -97.83 REMARK 500 PRO A 176 -76.69 -30.63 REMARK 500 SER A 190 -145.17 -152.56 REMARK 500 VAL A 207 -14.99 -142.38 REMARK 500 ASP A 214 140.88 161.76 REMARK 500 ASP A 230 -163.44 -160.77 REMARK 500 GLU A 235 -69.35 -29.13 REMARK 500 TRP A 236 8.25 -61.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KK8 RELATED DB: PDB REMARK 900 RELATED ID: 3KL8 RELATED DB: PDB DBREF 3KK9 A 7 288 UNP Q9U6Q0 Q9U6Q0_CAEEL 6 287 SEQADV 3KK9 ASN A 135 UNP Q9U6Q0 ASP 134 ENGINEERED MUTATION SEQRES 1 A 282 THR LYS PHE SER ASP ASN TYR ASP VAL LYS GLU GLU LEU SEQRES 2 A 282 GLY LYS GLY ALA PHE SER VAL VAL ARG ARG CYS VAL HIS SEQRES 3 A 282 LYS THR THR GLY LEU GLU PHE ALA ALA LYS ILE ILE ASN SEQRES 4 A 282 THR LYS LYS LEU SER ALA ARG ASP PHE GLN LYS LEU GLU SEQRES 5 A 282 ARG GLU ALA ARG ILE CYS ARG LYS LEU GLN HIS PRO ASN SEQRES 6 A 282 ILE VAL ARG LEU HIS ASP SER ILE GLN GLU GLU SER PHE SEQRES 7 A 282 HIS TYR LEU VAL PHE ASP LEU VAL THR GLY GLY GLU LEU SEQRES 8 A 282 PHE GLU ASP ILE VAL ALA ARG GLU PHE TYR SER GLU ALA SEQRES 9 A 282 ASP ALA SER HIS CYS ILE GLN GLN ILE LEU GLU SER ILE SEQRES 10 A 282 ALA TYR CYS HIS SER ASN GLY ILE VAL HIS ARG ASN LEU SEQRES 11 A 282 LYS PRO GLU ASN LEU LEU LEU ALA SER LYS ALA LYS GLY SEQRES 12 A 282 ALA ALA VAL LYS LEU ALA ASP PHE GLY LEU ALA ILE GLU SEQRES 13 A 282 VAL ASN ASP SER GLU ALA TRP HIS GLY PHE ALA GLY THR SEQRES 14 A 282 PRO GLY TYR LEU SER PRO GLU VAL LEU LYS LYS ASP PRO SEQRES 15 A 282 TYR SER LYS PRO VAL ASP ILE TRP ALA CYS GLY VAL ILE SEQRES 16 A 282 LEU TYR ILE LEU LEU VAL GLY TYR PRO PRO PHE TRP ASP SEQRES 17 A 282 GLU ASP GLN HIS ARG LEU TYR ALA GLN ILE LYS ALA GLY SEQRES 18 A 282 ALA TYR ASP TYR PRO SER PRO GLU TRP ASP THR VAL THR SEQRES 19 A 282 PRO GLU ALA LYS SER LEU ILE ASP SER MET LEU THR VAL SEQRES 20 A 282 ASN PRO LYS LYS ARG ILE THR ALA ASP GLN ALA LEU LYS SEQRES 21 A 282 VAL PRO TRP ILE CYS ASN ARG GLU ARG VAL ALA SER ALA SEQRES 22 A 282 ILE HIS ARG GLN ASP TPO VAL ASP CYS MODRES 3KK9 TPO A 285 THR PHOSPHOTHREONINE HET TPO A 285 11 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 TPO C4 H10 N O6 P HELIX 1 1 LYS A 8 ASN A 12 1 5 HELIX 2 2 SER A 50 LEU A 67 1 18 HELIX 3 3 GLU A 96 GLU A 105 1 10 HELIX 4 4 SER A 108 ASN A 129 1 22 HELIX 5 5 THR A 175 LEU A 179 5 5 HELIX 6 6 SER A 180 LYS A 185 1 6 HELIX 7 7 LYS A 191 GLY A 208 1 18 HELIX 8 8 ASP A 216 GLY A 227 1 12 HELIX 9 9 PRO A 234 THR A 238 5 5 HELIX 10 10 THR A 240 LEU A 251 1 12 HELIX 11 11 THR A 260 LEU A 265 1 6 HELIX 12 12 VAL A 267 ASN A 272 1 6 SHEET 1 A 5 TYR A 13 GLY A 22 0 SHEET 2 A 5 SER A 25 HIS A 32 -1 O ARG A 29 N LYS A 16 SHEET 3 A 5 GLU A 38 ASN A 45 -1 O PHE A 39 N CYS A 30 SHEET 4 A 5 PHE A 84 ASP A 90 -1 O PHE A 89 N ALA A 40 SHEET 5 A 5 LEU A 75 GLU A 81 -1 N HIS A 76 O VAL A 88 SHEET 1 B 2 ILE A 131 VAL A 132 0 SHEET 2 B 2 ILE A 161 GLU A 162 -1 O ILE A 161 N VAL A 132 SHEET 1 C 2 LEU A 141 LEU A 143 0 SHEET 2 C 2 VAL A 152 LEU A 154 -1 O LYS A 153 N LEU A 142 LINK C ASP A 284 N TPO A 285 1555 1555 1.33 LINK C TPO A 285 N VAL A 286 1555 1555 1.33 CISPEP 1 SER A 233 PRO A 234 0 3.22 CRYST1 37.708 60.470 70.243 90.00 93.92 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026520 0.000000 0.001819 0.00000 SCALE2 0.000000 0.016537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014270 0.00000